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Generating 2D Coords does not work with 3D structures [message #1244]

Mon, 08 March 2021 11:56

richards99
Messages: 42
Registered: May 2020
Location: UK

Member

It seems that when I what to regenerate 2D coordinates for structures from Chemistry/Generate 2D Coordinates, and provide a Substructure to align too, this does not seem to work if the structures already have 3D coordinates.

Workaround currently, is I generated SMILES of these structures, do Name to Structure, and then generate 2D coordinates on these.

Simon.

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Re: Generating 2D Coords does not work with 3D structures [message #1246 is a reply to message #1244]

Tue, 09 March 2021 17:20

thomas
Messages: 731
Registered: June 2014

Senior Member

Thank you. There was an issue of not applying a template's 2d-atom-coordinates, if the template consisted of the same atoms that were later automatically discovered as part of a fragment coordinate rule within the coordinate inventor (e.g. a ring or a connecting chain. This is now fixed in the current development version. If you still have issues, please send me a reproducible example. Whether 3D-coordinates exist should not make a difference.

Thomas

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